In the Gulf War flashback at the very start, the soldiers fire their rifles in fully automatic fire mode. In reality, the US Army and USMC standard issue rifle during the Gulf War was the M16A2. The M16A2 can only fire in semi-automatic or three-round burst modes. This is a very common mistake in movies and TV-series.
In an early scene with Skinner and Scully talking in a hallway, there is a visible crew member hiding behind a trash can.
Scully refers to Lt. Josepho's Bible verse (about the four angelic visitors) as "Ephesians," a New Testament epistle by Saint Paul. The quotation is actually from Ezekiel, a prophetic memoir from the Old Testament.
When Josepho is calling in his contact report, he makes the same old Hollywood error of using the word 'REPEAT' over the radio. The correct terminology to use is "I SAY AGAIN' and you only do so if the person you're talking to asks for a confirmation of your message. It is an age old Hollywood cliché that, whenever a character speaks on a radio, they have to relay the message twice to accentuate the drama.